Extensive C->U transition biases in the genomes of a wide range of mammalian RNA viruses; potential associations with transcriptional mutations, damage- or host-mediated editing of viral RNAResearch Article Published on 2021-06-012022-10-29 Journal: PLoS Pathogens [Category] COVID-19, MERS, SARS, [키워드] accounted adaptive aligned ANOVA antiretroviral APOBEC association Caliciviridae change coding region Combination component contribute Coronaviridae dataset disease driven by Evidence Evolution Extensive fixation Flaviviridae Frequency Generation time genetic change Genome genome sequence genomes genomic HCV HIV-1 homoplasy identity infecting investigated mammalian mammals mechanism mechanisms multivariable analysis Mutation mutations Neutral Occurrence parameter phylogenetically provide random replicate Replication reported representing retrovirus RNA RNA secondary structure RNA virus RNA viruses SARS Coronavirus SARS-CoV-2 sequence sequence variability significantly subset Substitution thought transcriptional upstream Viral RNA virus while [DOI] 10.1371/journal.ppat.1009596 PMC 바로가기 [Article Type] Research Article
In Vivo and In Vitro Genome-Wide Profiling of RNA Secondary Structures Reveals Key Regulatory Features in Plasmodium falciparum플라스모디움 팔시파룸에서 RNA 2차 구조의 생체 내 및 시험관 내 유전체 전반 프로파일링이 주요 조절 기능을 밝혀냄Original Research Published on 2021-05-172024-08-08 Journal: Frontiers in Cellular and Infection Microbiology [Category] 말라리아, [키워드] in vitro in vivo mRNA Plasmodium falciparum RNA secondary structure [DOI] 10.3389/fcimb.2021.673966 PMC 바로가기 [Article Type] Original Research
Developing effective siRNAs to reduce the expression of key viral genes of COVID-19COVID-19의 주요 바이러스 유전자 발현을 감소시키는 효과적인 siRNA 개발Research Paper Published on 2021-04-102022-09-10 Journal: International Journal of Biological Sciences [Category] MERS, SARS, 변종, 치료법, [키워드] 24 hours antiviral drug antiviral drugs binding efficiency can be used clinical development Consensus COVID-19 COVID-19 pandemic degrade develop Developing effective Efficiency effort Endothelial cell endothelial cells expression gene silencing human lung medication membrane nucleocapsid overexpressing PBE Probability provide reduce reducing Region RNA RNA molecules RNA secondary structure SARS-CoV-2 secondary structure secondary structures significantly siRNA siRNAs suggested target gene Target genes the disease Vaccine Viral viral gene viral genes viral genome viral infection [DOI] 10.7150/ijbs.59151 PMC 바로가기 [Article Type] Research Paper
Indels in SARS-CoV-2 occur at template-switching hotspotsResearch Published on 2021-03-202022-10-28 Journal: BioData Mining [Category] COVID-19, [키워드] Analysis breakpoint consensus sequence consensus sequences consequence COVID-19 pandemic de novo Deletion Evidence evolutionary dynamics Genome Genomics GISAID GISAID database heterogeneity homogeneity homologous Host hotspot IMPROVE INDEL indels independent insertion loci mechanism occur other coronaviruses predicted raw reads RdRP Recombination recombination event Region Regulatory replicate RNA RNA secondary structure RNA virus RNA viruses RNA-dependent RNA polymerase SARS-CoV-2 SARS-CoV-2 evolution secondary structure sequence Single nucleotide polymorphism Structural variation Structure supplementary material the SARS-CoV-2 Transcription Transcriptome TRS [DOI] 10.1186/s13040-021-00251-0 PMC 바로가기 [Article Type] Research
Targeting the DEAD-Box RNA Helicase eIF4A with Rocaglates—A Pan-Antiviral Strategy for Minimizing the Impact of Future RNA Virus PandemicsReview Published on 2021-03-052022-10-29 Journal: Microorganisms [Category] COVID-19, [키워드] Antiviral broad-spectrum antiviral broad-spectrum antivirals candidate caused cellular complex Compound coronavirus COVID-19 CR-31-B drug eIF4A eukaryotic translation exhibiting fraction Future Helicase highlight host mRNA Impact increase in inhibitors inhibitory effect interactions Intervention limit maintaining mechanism of action mRNA outbreak pan-antiviral Pandemics protein synthesis Region Replication resulting RNA RNA secondary structure RNA virus RNA viruses rocaglates safety profile sequence Side effects silvestrol Strategy targeting therapeutic translation translation initiation unique Vaccine viral mRNA zoonotic origin Zotatifin [DOI] 10.3390/microorganisms9030540 PMC 바로가기 [Article Type] Review
In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugsArticle Published on 2021-02-092023-06-18 Journal: Cell [Category] Fulltext, SARS, [키워드] drug reproposing Host factor RBP binding prediction RNA secondary structure SARS-CoV-2 [DOI] 10.1016/j.cell.2021.02.008 PMC 바로가기 [Article Type] Article
Isolating SARS-CoV-2 Strains From Countries in the Same Meridian: Genome Evolutionary AnalysisOriginal Paper Published on 2021-01-222022-10-29 Journal: Jmir Bioinformatics and Biotechnology [Category] COVID-19, [키워드] 3D Structures acting affected Algorithm analyses Analysis analyzed Antiviral strategies approach Asia average binding binding probability Brazil caused change characterized clade clinical feature codon codon mutation Codons conditions country COVID-19 death Effect ENCODE ENhance epidemiological episodic selective pressure eukaryotic cells Europe Evolution Evolutionary analysis facilitate Genetic genetics Genome genomes genomic glycine help in vitro experiment initiative Isolating Italy Modification mutated Mutation North America objective ontological Ontology performed Phylogenetic tree positioned predict predicted prediction pressure Probability Protein Recombination reported Repository respiratory infection responsible Result RNA secondary structure SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 strain secondary structure selective sequence shown similarity strain Structure to define transmembrane transmembrane region turn Vaccine design virus Virus evolution wild-type [DOI] 10.2196/25995 PMC 바로가기 [Article Type] Original Paper
Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanismsArticle Published on 2021-01-012023-06-16 Journal: Molecular Cell [Category] MERS, [키워드] chemical probing coronavirus locked nucleic acids riboregulation RNA genome RNA motif RNA secondary structure RNA structure RNA virus SHAPE-MaP [DOI] 10.1016/j.molcel.2020.12.041 PMC 바로가기 [Article Type] Article
Pervasive RNA Secondary Structure in the Genomes of SARS-CoV-2 and Other CoronavirusesResearch Article Published on 2020-10-302022-10-29 Journal: mBio [Category] COVID-19, MERS, SARS, [키워드] acute respiratory syndrome analyzed arise association Cell cellular interaction coding sequences complex interplay conserved contribute coronavirus coronavirus disease coronavirus genome COVID-19 dependent on element Evidence Evolution examined Features Genome greater HCV hepatitis C virus homologous Host Human identity immune dysfunction include infecting influence investigated less mammals Molecular epidemiology Mutation Other other coronavirus outcome pandemic pathogenicity persistence population immunity positioned possession predicted Prevent Prolonged infection protective immunity related viruses RNA RNA secondary structure RNA virus RNA viruses SARS-CoV SARS-CoV-2 secondary sequence shielding Site Structure Transmissibility Transmission Viral RNA virus [DOI] 10.1128/mBio.01661-20 PMC 바로가기 [Article Type] Research Article
Similarity between mutation spectra in hypermutated genomes of rubella virus and in SARS-CoV-2 genomes accumulated during the COVID-19 pandemic풍진 바이러스의 과돌연변이된 게놈과 COVID-19 전염병 동안 축적된 SARS-CoV-2 게놈의 돌연변이 스펙트럼 간의 유사성Research Article Published on 2020-10-022022-08-13 Journal: PLoS ONE [Category] MERS, SARS, 유전자 메커니즘, [키워드] accumulated accumulation Analysis APOBEC cytidine deaminase change characteristic COVID-19 pandemic cytidine Cytidine deaminase dataset Each enrichment event genomes genomic RNA human population hypermutated genome hypermutated genomes hypermutation individual isolate lead motif Mutation mutation mechanism mutation mechanisms mutational spectrum new SARS-CoV-2 pathological condition positive predicted preference Propagation reported RNA secondary structure RNA virus rubella rubella vaccine rubella vaccine virus rubella virus SARS-CoV-2 SARS-CoV-2 genome SARS-CoV-2 mutation SARS-CoV-2 viruses SARS-CoV2 secondary structure sequenced similarity single base substitution single base substitutions single subject strand genomic RNA subclass substitutions suggested the SARS-CoV-2 virus virus isolate viruses [DOI] 10.1371/journal.pone.0237689 PMC 바로가기 [Article Type] Research Article